Cytotoxicity Mediated by the Fas Ligand (FasL)-activated Apoptotic Pathway in Stem Cells

Whereas it is now clear that human bone marrow stromal cells (BMSCs) can be immunosuppressive and escape cytotoxic lymphocytes (CTLs) in vitro and in vivo, the mechanisms of this phenomenon remain controversial. Here, we test the hypothesis that BMSCs suppress immune responses by Fas-mediated apoptosis of activated lymphocytes and find both Fas and FasL expression by primary BMSCs. Jurkat cells or activated lymphocytes were each killed by BMSCs after 72 h of co-incubation. In comparison, the cytotoxic effect of BMSCs on non-activated lymphocytes and on caspase-8(−/−) Jurkat cells was extremely low. Fas/Fc fusion protein strongly inhibited BMSC-induced lymphocyte apoptosis. Although we detected a high level of Fas expression in BMSCs, stimulation of Fas with anti-Fas antibody did not result in the expected BMSC apoptosis, regardless of concentration, suggesting a disruption of the Fas activation pathway. Thus BMSCs may have an endogenous mechanism to evade Fas-mediated apoptosis. Cumulatively, these data provide a parallel between adult stem/progenitor cells and cancer cells, consistent with the idea that stem/progenitor cells can use FasL to prevent lymphocyte attack by inducing lymphocyte apoptosis during the regeneration of injured tissues.Human bone marrow stromal cells (BMSCs)² (also referred to as mesenchymal stem cells (MSCs)) (1) contain a subset of multipotent, non-hematopoietic stem/progenitor cells. BMSCs can differentiate into hematopoiesis-supporting stromal tissue, adipocytes, osteoblasts, and chondrocytes (2, 3). In addition, they may be able to transdifferentiate into hepatocytes, myocytes, neuroectodermal cells, and endothelial cells, (4–6) although proof of such differentiation is not definitive to date. BMSCs have immunosuppressive potential, as recently demonstrated in both in vitro (7) and in vivo (8, 9) systems, including clinical studies (10, 11). However, the mechanisms by which BMSCs suppress immune responses are unresolved. Soluble factor-mediated immunosuppressive effects are beginning to come to light, (10, 12), and in addition there are as yet unexplained effects of cell-to-cell contact.In the present study, we hypothesize that BMSC-mediated cytotoxicity of lymphocytes involves the FasL-activated apoptotic machinery. FasL is a type II transmembrane protein belonging to the tumor necrosis factor (TNF) family. FasL interacts with its receptor, Fas (CD95/APO-1) and triggers a cascade of subcellular events culminating in apoptotic cell death. FasL and Fas are key regulators of apoptosis in the immune system. In addition, FasL is expressed by cells in immune-privileged sites, such as cancer cells, neurons, eyes, cytotrophoblasts of the placenta, and reproductive organs (13–17). In neurons, FasL expression specifically protects against T cell-mediated cytotoxicity (16).The discovery that FasL is also expressed by a variety of tumor cells raises the possibility that FasL may mediate immune privilege in human tumors (18). Activated T cells expressing Fas are sensitive to Fas-mediated apoptosis. Thus, up-regulation of FasL expression by tumor cells may enable tumorigenesis by targeting apoptosis in infiltrating lymphocytes. In the present work, we show that BMSCs can mediate immunosuppressive activity by FasL-induced killing of activated lymphocytes. Thus, BMSCs have properties of immune-privileged cells.     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Algorithms for Finding Small Attractors in Boolean Networks

A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Structural and Quantitative Evidence for Dynamic Glycome Shift on Production of Induced Pluripotent Stem Cells

We recently reported that induced pluripotent stem cells (iPSCs) prepared from different human origins acquired similar glycan profiles to one another as well as to human embryonic stem cells. Although the results strongly suggested attainment of specific glycan expressions associated with the acquisition of pluripotency, the detailed glycan structures remained to be elucidated. Here, we perform a quantitative glycome analysis targeting both N- and O-linked glycans derived from 201B7 human iPSCs and human dermal fibroblasts as undifferentiated and differentiated cells, respectively. Overall, the fractions of high mannose-type N-linked glycans were significantly increased upon induction of pluripotency. Moreover, it became evident that the type of linkage of Sia on N-linked glycans was dramatically changed from α-2–3 to α-2–6, and the expression of α-1–2 fucose and type 1 LacNAc structures became clearly apparent, while no such glycan epitopes were detected in fibroblasts. The expression profiles of relevant glycosyltransferase genes were fully consistent with these results. These observations indicate unambiguously the manifestation of a “glycome shift” upon conversion to iPSCs, which may not merely be the result of the initialization of gene expression, but could be involved in a more aggressive manner either in the acquisition or maintenance of the undifferentiated state of iPSCs.Induced pluripotent stem cells (iPSCs)¹ are genetically manufactured pluripotent cells obtained by the transfection of reprogramming factors. Such iPSCs were first reported in 2006 for the mouse (1) and in 2007 for humans (2, 3). Although iPSCs have already been used in the fields of drug development and disease models (4–7), basic aspects of iPSCs largely remain to be elucidated to provide us with a fuller understanding of their properties and for therapeutic applications to be developed in the field of regenerative medicine. These aspects include the need for a definitive system to be established to evaluate their properties; e.g. pluripotency, differentiation propensity, risk of possible contamination of xenoantigens, and even the potential for tumorigenesis. Cell surface glycans are often referred to as the “cell signature,” which changes dramatically depending on the cell properties and conditions (8) as a result of changes in gene expression, including epigenetic modifications of glycan-related molecules. Glycans, because of their outermost cell-surface locations and structural complexity, are considered to be most advantageous communication molecules, playing roles in various biological phenomena. Indeed, SSEA3/4 and Tra-1–60/81, which have been used to discriminate pluripotency, are cell surface glycan epitopes that respond to some specific antibodies (9–12).Glycan-mediated cell-to-cell interactions have been shown to play important roles in various biological phenomena including embryogenesis and carcinogenesis (13–16). This might also be the case for the acquisition and maintenance of iPSC and ESC pluripotency, although there remains much to clarify concerning the roles of cell surface glycans in these events. Thus, the development of novel cell surface markers to evaluate the properties of iPSCs and ESCs is keenly required. Toward this goal, a glycomic approach has been made by several groups (17–20). In our previous study using an advanced lectin microarray technique (21), thirty-eight lectins capable of discriminating between iPSCs and SCs were statistically selected, and the characteristic features of the pluripotent state were obtained. The glycan profiles of the parent SCs, derived from four different tissues, were totally different from one another and from those of the iPSCs. Despite this observation, the technique used lacks the ability to determine detailed glycan structures or allow their quantification. For this purpose, a conventional approach based on high performance liquid chromatography (HPLC) combined with matrix-assisted laser desorption-ionization (MALDI) - time of flight (TOF) mass spectrometry (MS) was undertaken for both the definitive identification of glycan structures and their quantitative comparison, which remained unclear in the previous analysis (21).We report here structural data on N-linked and O-linked glycans derived from the human iPSC 201B7 cell line (2) and human dermal fibroblasts (SC) representing undifferentiated and differentiated cells, respectively. For quantitative comparison, the glycans were liberated by gas-phase hydrazinolysis from similar numbers of cells (22–25) fluorescently tagged with 2-aminopyridine (2-AP) at their reducing terminus (26, 27), following which the derived pyridylaminated (PA-) glycans were purified by multiple-mode (i.e. anion-exchange, size-fractionation and reverse-phase) HPLC. Their structures were determined and quantified by HPLC mapping assisted with MALDI-TOF-MS and exoglycosidase digestion analyses. This report thus provides the first structural evidence showing the occurrence of a dynamic “glycome shift” upon induction of pluripotency.     

Targeting proapoptotic protein BAD inhibits survival and self-renewal of cancer stem cells

Emerging evidence suggests that the resistance of cancer stem cells (CSC) to many conventional therapies is one of the major limiting factors of cancer therapy efficacy. Identification of mechanisms responsible for survival and self-renewal of CSC will help design new therapeutic strategies that target and eliminate both differentiated cancer cells and CSC. Here we demonstrated the potential role of proapoptotic protein BAD in the biology of CSC in melanoma, prostate and breast cancers. We enriched CD44⁺/CD24⁻ cells (CSC) by tumorosphere formation and purified this population by FACS. Both spheres and CSC exhibited increased potential for proliferation, migration, invasion, sphere formation, anchorage-independent growth, as well as upregulation of several stem cell-associated markers. We showed that the phosphorylation of BAD is essential for the survival of CSC. Conversely, ectopic expression of a phosphorylation-deficient mutant BAD induced apoptosis in CSC. This effect was enhanced by treatment with a BH3-mimetic, ABT-737. Both pharmacological agents that inhibit survival kinases and growth factors that are involved in drug resistance delivered their respective cytotoxic and protective effects by modulating the BAD phosphorylation in CSC. Furthermore, the frequency and self-renewal capacity of CSC was significantly reduced by knocking down the BAD expression. Consistent with our in vitro results, significant phosphorylation of BAD was found in CD44⁺ CSC of 83% breast tumor specimens. In addition, we also identified a positive correlation between BAD expression and disease stage in prostate cancer, suggesting a role of BAD in tumor advancement. Our studies unveil the role of BAD in the survival and self-renewal of CSC and propose BAD not only as an attractive target for cancer therapy but also as a marker of tumor progression.Although tumors initially respond positively to anti-cancer agents, several cancers, despite the best care and significant improvements in treatment, recur and progress to advanced stages of the disease. The mechanisms underlying this recurrence and metastasis are not clearly understood. Over the past decade, substantial evidence supported the cancer stem cell (CSC) hypothesis as a viable explanation for the initiation, progression and recurrence of cancer. According to this hypothesis, each tumor harbors a small subpopulation of specialized cells among cellular heterogeneity, known as CSC. These cells exhibit self-renewal property that drives tumorigenesis and plasticity to differentiate into multiple cell types contributing to tumor cellular heterogeneity. Support for this hypothesis came from the studies by Lapidot et al. who identified tumor-initiating cells in acute myeloid leukemia.^{1, 2} Subsequently, CSCs have been identified in several cancers.^{3, 4, 5, 6, 7, 8, 9, 10}Accumulating evidence suggests that current cancer therapies can only shrink tumors as they target and kill the differentiated cancer (DC) cells, but are unable to target the rare CSC population.^{11, 12} Thus, despite a wealth of information on DC cells, the active survival and self-renewal pathways in CSCs have not been characterized thoroughly. An understanding of the molecular mechanisms involved in the survival, self-renewal and resistance of CSCs to current therapeutic regimens is of immense clinical interest. This information will help in developing novel strategies for more effective treatments for cancer.Most anti-cancer drugs exert their effects through triggering the apoptotic pathways. However, malignant cancer cells can escape apoptosis by altering the expression level of proapoptotic and antiapoptotic BCL-2 family members. Considering the potential role of BCL-2 family members in tumorigenesis and cancer cell survival, their role in CSC biology has been increasingly studied.^{13, 14} BAD (BCL2-antagonist of cell death) is a member of the BH3-only BCL-2 family protein that when dephosphorylated promotes apoptosis by heterodimerizing with the antiapoptotic proteins BCL-XL and BCL-2.¹⁵ The cytotoxic effects of BAD are controlled by mechanisms that regulate its phosphorylation on at least two distinct serine residues, S112 and S136.^{16, 17, 18} Previously, we showed that phosphorylation at either site is sufficient to protect prostate cancer cells from apoptosis.^{19, 20, 21} We also showed that BAD promotes prostate tumor growth in mouse models.²² Clinically, while BAD expression was associated with relapse in tamoxifen-treated breast cancer patients,^{23, 24} phospho-BAD expression was associated with cisplatin resistance and poor overall survival in ovarian cancer.²⁵Our previous findings along with other reports showing the role of BAD in the apoptosis modulation and growth of DC cells^{19, 22, 26} prompted us to explore the potential role of BAD in the biology of CSCs. We started our investigation by assessing the role of BAD in survival and self-renewal of CSCs. As we observed a significant role for BAD in CSC''s biology, we extended our work to assess the BAD phosphorylation in CSCs of breast cancer patient tumors and for a potential correlation between BAD expression and disease progression in prostate cancer.     

The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be problematic. One challenge is the comparison of temporal expression data obtained from different growth conditions where the patterns of expression may be shifted in time. We propose the use of wavelet analysis to transform the data obtained under different growth conditions to permit comparison of expression patterns from experiments that have time shifts or delays. We demonstrate this approach using detailed temporal data for a single bacterial gene obtained under 72 different growth conditions. This general strategy can be applied in the analysis of data sets of thousands of genes under different conditions.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]